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   <h1>Python Module Index</h1>

   <div class="modindex-jumpbox">
   <a href="#cap-a"><strong>a</strong></a> | 
   <a href="#cap-c"><strong>c</strong></a> | 
   <a href="#cap-d"><strong>d</strong></a> | 
   <a href="#cap-e"><strong>e</strong></a> | 
   <a href="#cap-f"><strong>f</strong></a> | 
   <a href="#cap-i"><strong>i</strong></a> | 
   <a href="#cap-l"><strong>l</strong></a> | 
   <a href="#cap-m"><strong>m</strong></a> | 
   <a href="#cap-n"><strong>n</strong></a> | 
   <a href="#cap-o"><strong>o</strong></a> | 
   <a href="#cap-p"><strong>p</strong></a> | 
   <a href="#cap-q"><strong>q</strong></a> | 
   <a href="#cap-r"><strong>r</strong></a> | 
   <a href="#cap-s"><strong>s</strong></a> | 
   <a href="#cap-t"><strong>t</strong></a> | 
   <a href="#cap-u"><strong>u</strong></a> | 
   <a href="#cap-v"><strong>v</strong></a>
   </div>

   <table class="indextable modindextable">
     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
     <tr class="cap" id="cap-a"><td></td><td>
       <strong>a</strong></td><td></td></tr>
     <tr>
       <td><img src="_static/minus.png" class="toggler"
              id="toggle-1" style="display: none" alt="-" /></td>
       <td>
       <code class="xref">ase</code></td><td>
       <em></em></td></tr>
     <tr class="cg-1">
       <td></td>
       <td>&#160;&#160;&#160;
       <a href="io.html#module-ase.io.extxyz"><code class="xref">ase.io.extxyz</code></a></td><td>
       <em>Python reference implementation of Extended XYZ I/O</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="atomeye.html#module-atomeye"><code class="xref">atomeye</code></a></td><td>
       <em>AtomEye atomistic configuration viewer</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="lotf.html#module-quippy.adjustablepotential"><code class="xref">quippy.adjustablepotential</code></a></td><td>
       <em>`Learn on the Fly` adjustable potential</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="io.html#module-quippy.asap"><code class="xref">quippy.asap</code></a></td><td>
       <em>ASAP file reader and writer</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="io.html#module-quippy.atomeyewriter"><code class="xref">quippy.atomeyewriter</code></a></td><td>
       <em>AtomEye image writer</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="atoms.html#module-quippy.atoms"><code class="xref">quippy.atoms</code></a></td><td>
       <em>Representation of atomic configurations</em></td></tr>
     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
     <tr class="cap" id="cap-c"><td></td><td>
       <strong>c</strong></td><td></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="io.html#module-quippy.castep"><code class="xref">quippy.castep</code></a></td><td>
       <em>CASTEP file readers and writers</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="io.html#module-quippy.cinoutput"><code class="xref">quippy.cinoutput</code></a></td><td>
       <em>XYZ and NetCDF I/O using fast C routines</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="clusters.html#module-quippy.clusters"><code class="xref">quippy.clusters</code></a></td><td>
       <em>Cluster carving routines</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="cp2k.html#module-quippy.cp2k"><code class="xref">quippy.cp2k</code></a></td><td>
       <em>CP2K I/O</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="cp2k.html#module-quippy.cp2k_driver"><code class="xref">quippy.cp2k_driver</code></a></td><td>
       <em>CP2K Interface</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="crack.html#module-quippy.crack"><code class="xref">quippy.crack</code></a></td><td>
       <em>Tools for fracture simulations</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="io.html#module-quippy.cube"><code class="xref">quippy.cube</code></a></td><td>
       <em>Gaussian CUBE I/O</em></td></tr>
     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
     <tr class="cap" id="cap-d"><td></td><td>
       <strong>d</strong></td><td></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="io.html#module-quippy.dan"><code class="xref">quippy.dan</code></a></td><td>
       <em>DAN visualisation code writer</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="dictionary.html#module-quippy.dictionary"><code class="xref">quippy.dictionary</code></a></td><td>
       <em>Fortran dictionary for storing key/value pairs</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="dynamicalsystem.html#module-quippy.dynamicalsystem"><code class="xref">quippy.dynamicalsystem</code></a></td><td>
       <em>Run molecular dynamics simulations</em></td></tr>
     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
     <tr class="cap" id="cap-e"><td></td><td>
       <strong>e</strong></td><td></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="elasticity.html#module-quippy.elasticity"><code class="xref">quippy.elasticity</code></a></td><td>
       <em>Elasticity calculations</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="electrostaticembed.html#module-quippy.electrostaticembed"><code class="xref">quippy.electrostaticembed</code></a></td><td>
       <em>Tools for electrostatic embedding</em></td></tr>
     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
     <tr class="cap" id="cap-f"><td></td><td>
       <strong>f</strong></td><td></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="f2py_wrapper_gen.html#module-f2py_wrapper_gen"><code class="xref">f2py_wrapper_gen</code></a></td><td>
       <em>Generate simplified Fortran 90 source suitable for f2py</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="f90doc.html#module-f90doc"><code class="xref">f90doc</code></a></td><td>
       <em>Read Fortan 90 sources and extract documenataion strings</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="farray.html#module-quippy.farray"><code class="xref">quippy.farray</code></a></td><td>
       <em>Fortran one-based array indexing</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="find_surface_atoms.html#module-quippy.find_surface_atoms"><code class="xref">quippy.find_surface_atoms</code></a></td><td>
       <em>identification of atoms on surfaces</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="fortranio.html#module-quippy.fortranio"><code class="xref">quippy.fortranio</code></a></td><td>
       <em>Fortran input/output</em></td></tr>
     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
     <tr class="cap" id="cap-i"><td></td><td>
       <strong>i</strong></td><td></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="io.html#module-quippy.imd"><code class="xref">quippy.imd</code></a></td><td>
       <em>IMD checkpoint reader</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="io.html#module-quippy.io"><code class="xref">quippy.io</code></a></td><td>
       <em>Read and write atomic configurations</em></td></tr>
     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
     <tr class="cap" id="cap-l"><td></td><td>
       <strong>l</strong></td><td></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="linearalgebra.html#module-quippy.linearalgebra"><code class="xref">quippy.linearalgebra</code></a></td><td>
       <em>Linear algebra rountines</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="lotf.html#module-quippy.lotf"><code class="xref">quippy.lotf</code></a></td><td>
       <em>`Learn on the Fly` dynamics</em></td></tr>
     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
     <tr class="cap" id="cap-m"><td></td><td>
       <strong>m</strong></td><td></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="mpi_context.html#module-quippy.mpi_context"><code class="xref">quippy.mpi_context</code></a></td><td>
       <em>MPI parallel interface</em></td></tr>
     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
     <tr class="cap" id="cap-n"><td></td><td>
       <strong>n</strong></td><td></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="io.html#module-quippy.netcdf"><code class="xref">quippy.netcdf</code></a></td><td>
       <em>Python reference implementation of NetCDF I/O</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="io.html#module-quippy.nmwiz"><code class="xref">quippy.nmwiz</code></a></td><td>
       <em></em></td></tr>
     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
     <tr class="cap" id="cap-o"><td></td><td>
       <strong>o</strong></td><td></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="oo_fortran.html#module-quippy.oo_fortran"><code class="xref">quippy.oo_fortran</code></a></td><td>
       <em>Fortran 90 derived-type support</em></td></tr>
     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
     <tr class="cap" id="cap-p"><td></td><td>
       <strong>p</strong></td><td></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="paramreader.html#module-quippy.paramreader"><code class="xref">quippy.paramreader</code></a></td><td>
       <em>Command line argument parser</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="periodictable.html#module-quippy.periodictable"><code class="xref">quippy.periodictable</code></a></td><td>
       <em>Element data</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="phonons.html#module-quippy.phonons"><code class="xref">quippy.phonons</code></a></td><td>
       <em>Evaluate phonons</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="polarization.html#module-quippy.polarization"><code class="xref">quippy.polarization</code></a></td><td>
       <em>Tools for polarizable potentials</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="potential.html#module-quippy.potential"><code class="xref">quippy.potential</code></a></td><td>
       <em>Evaluate interatomic potentials</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="io.html#module-quippy.povray"><code class="xref">quippy.povray</code></a></td><td>
       <em>POV-ray script writer</em></td></tr>
     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
     <tr class="cap" id="cap-q"><td></td><td>
       <strong>q</strong></td><td></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="qlab.html#module-qlab"><code class="xref">qlab</code></a></td><td>
       <em>Interactive visualisation of atomic systems</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="index.html#module-quippy"><code class="xref">quippy</code></a></td><td>
       <em></em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="qpxml.html#module-quippy.qpxml"><code class="xref">quippy.qpxml</code></a></td><td>
       <em>Functions for manipulating GAP xml</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="quaternions.html#module-quippy.quaternions"><code class="xref">quippy.quaternions</code></a></td><td>
       <em>Quaternions and rotation</em></td></tr>
     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
     <tr class="cap" id="cap-r"><td></td><td>
       <strong>r</strong></td><td></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="real_space_covariance.html#module-quippy.real_space_covariance"><code class="xref">quippy.real_space_covariance</code></a></td><td>
       <em>Representation of atomic environments</em></td></tr>
     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
     <tr class="cap" id="cap-s"><td></td><td>
       <strong>s</strong></td><td></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="simplex.html#module-quippy.simplex"><code class="xref">quippy.simplex</code></a></td><td>
       <em>Nelder and Mead minimisation algorithm</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="spline.html#module-quippy.spline"><code class="xref">quippy.spline</code></a></td><td>
       <em>Cubic spline interpolation</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="structures.html#module-quippy.structures"><code class="xref">quippy.structures</code></a></td><td>
       <em>Structure building routines</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="system.html#module-quippy.system"><code class="xref">quippy.system</code></a></td><td>
       <em>Low-level routines</em></td></tr>
     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
     <tr class="cap" id="cap-t"><td></td><td>
       <strong>t</strong></td><td></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="table.html#module-quippy.table"><code class="xref">quippy.table</code></a></td><td>
       <em>Fortran type for dynamically extendable arrays</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="topology.html#module-quippy.topology"><code class="xref">quippy.topology</code></a></td><td>
       <em>utilities for topological analysis</em></td></tr>
     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
     <tr class="cap" id="cap-u"><td></td><td>
       <strong>u</strong></td><td></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="units.html#module-quippy.units"><code class="xref">quippy.units</code></a></td><td>
       <em>Units and physical constants</em></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="util.html#module-quippy.util"><code class="xref">quippy.util</code></a></td><td>
       <em>Python utility functions</em></td></tr>
     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
     <tr class="cap" id="cap-v"><td></td><td>
       <strong>v</strong></td><td></td></tr>
     <tr>
       <td></td>
       <td>
       <a href="io.html#module-quippy.vasp"><code class="xref">quippy.vasp</code></a></td><td>
       <em>VASP POSCAR and OUTCAR readers and writers</em></td></tr>
   </table>


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